TY - JOUR
T1 - Accurate detection of circulating tumor DNA using nanopore consensus sequencing
AU - Marcozzi, Alessio
AU - Jager, Myrthe
AU - Elferink, Martin
AU - Straver, Roy
AU - van Ginkel, Joost H
AU - Peltenburg, Boris
AU - Chen, Li-Ting
AU - Renkens, Ivo
AU - van Kuik, Joyce
AU - Terhaard, Chris
AU - de Bree, Remco
AU - Devriese, Lot A
AU - Willems, Stefan M
AU - Kloosterman, Wigard P
AU - de Ridder, Jeroen
N1 - Funding Information:
We would like to thank Manon Huibers for input on the study, Floris Reinders for input on the manuscript and the Utrecht Sequencing Facility for sequencing. The Utrecht Sequencing Facility is subsidized by the University Medical Center Utrecht, Hubrecht Institute, and Utrecht University. This study was financially supported by the Oncode Institute (project number P2018-004) and is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/9
Y1 - 2021/12/9
N2 - Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ~60×, enabling accurate detection of TP53 mutations at frequencies down to 0.02%. We demonstrate that a TP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in clinical workflows.
AB - Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ~60×, enabling accurate detection of TP53 mutations at frequencies down to 0.02%. We demonstrate that a TP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in clinical workflows.
UR - http://www.scopus.com/inward/record.url?scp=85121034107&partnerID=8YFLogxK
U2 - 10.1038/s41525-021-00272-y
DO - 10.1038/s41525-021-00272-y
M3 - Article
C2 - 34887408
VL - 6
SP - 1
EP - 11
JO - npj Genomic Medicine
JF - npj Genomic Medicine
IS - 1
M1 - 106
ER -